Rilpivirine/Tanofivir HPLC method validation

library(readxl)
library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(ggplot2)
library(plotly)

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
## 
##     layout

library(RColorBrewer)
library(rstudioapi)

## Warning: package 'rstudioapi' was built under R version 4.1.1

this.dir = rstudioapi::getActiveDocumentContext()$path
setwd(dirname(this.dir))
data.filename = 'Nina_TAF_RPV_20230201.XLS'
data.tanofivir = read_xls(data.filename,
                range='B6:J38',
                col_types = c('numeric', 'skip', 'skip', 'text', 'guess',
                              'numeric', 'numeric', 'skip', 'numeric'))

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B7 / R7C2: '4'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G7 / R7C7: '4.877'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J7 / R7C10: '1145.3029'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B8 / R8C2: '5'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G8 / R8C7: '4.894'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J8 / R8C10: '682.2532'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B9 / R9C2: '6'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G9 / R9C7: '4.905'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J9 / R9C10: '405.9534'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B10 / R10C2: '7'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G10 / R10C7: '4.913'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J10 / R10C10: '233.3646'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B11 / R11C2: '8'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G11 / R11C7: '4.919'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J11 / R11C10: '126.4434'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B12 / R12C2: '9'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G12 / R12C7: '4.926'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J12 / R12C10: '64.2587'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B13 / R13C2: '10'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G13 / R13C7: '4.927'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J13 / R13C10: '31.0484'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B14 / R14C2: '11'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G14 / R14C7: '4.928'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J14 / R14C10: '13.5178'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B15 / R15C2: '12'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G15 / R15C7: '4.927'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J15 / R15C10: '5.7271'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B16 / R16C2: '13'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G16 / R16C7: '4.930'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J16 / R16C10: '2.0695'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B17 / R17C2: '14'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B18 / R18C2: '15'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B19 / R19C2: '16'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B20 / R20C2: '17'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G20 / R20C7: '4.874'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J20 / R20C10: '1174.9629'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B21 / R21C2: '18'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G21 / R21C7: '4.894'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J21 / R21C10: '685.8564'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B22 / R22C2: '19'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G22 / R22C7: '4.908'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J22 / R22C10: '408.3145'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B23 / R23C2: '20'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G23 / R23C7: '4.917'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J23 / R23C10: '242.0120'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B24 / R24C2: '21'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G24 / R24C7: '4.922'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J24 / R24C10: '131.3083'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B25 / R25C2: '22'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G25 / R25C7: '4.926'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J25 / R25C10: '66.6893'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B26 / R26C2: '23'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G26 / R26C7: '4.931'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J26 / R26C10: '32.2542'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B27 / R27C2: '24'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G27 / R27C7: '4.932'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J27 / R27C10: '14.2579'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B28 / R28C2: '25'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G28 / R28C7: '4.934'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J28 / R28C10: '5.8964'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B29 / R29C2: '26'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G29 / R29C7: '4.933'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J29 / R29C10: '2.3528'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B30 / R30C2: '27'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B31 / R31C2: '28'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B32 / R32C2: '29'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B33 / R33C2: '30'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G33 / R33C7: '4.904'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J33 / R33C10: '514.4330'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B34 / R34C2: '31'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G34 / R34C7: '4.901'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J34 / R34C10: '561.7248'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B35 / R35C2: '32'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G35 / R35C7: '4.931'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J35 / R35C10: '31.7004'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B36 / R36C2: '33'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G36 / R36C7: '4.931'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J36 / R36C10: '33.0279'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B37 / R37C2: '34'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G37 / R37C7: '4.932'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J37 / R37C10: '11.7121'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B38 / R38C2: '35'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G38 / R38C7: '4.932'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J38 / R38C10: '11.2958'

data.rilpivirine = read_xls(data.filename,
                            range = 'B80:J112',
                            col_types = c('numeric', 'skip', 'skip', 'text', 'guess',
                              'numeric', 'numeric', 'skip', 'numeric'))

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B81 / R81C2: '4'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G81 / R81C7: '4.406'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J81 / R81C10: '336.2256'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B82 / R82C2: '5'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G82 / R82C7: '4.415'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J82 / R82C10: '186.5480'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B83 / R83C2: '6'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G83 / R83C7: '4.422'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J83 / R83C10: '98.8344'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B84 / R84C2: '7'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G84 / R84C7: '4.425'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J84 / R84C10: '50.6912'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B85 / R85C2: '8'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G85 / R85C7: '4.428'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J85 / R85C10: '25.5788'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B86 / R86C2: '9'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G86 / R86C7: '4.432'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J86 / R86C10: '12.7343'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B87 / R87C2: '10'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G87 / R87C7: '4.433'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J87 / R87C10: '6.5805'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B88 / R88C2: '11'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G88 / R88C7: '4.432'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J88 / R88C10: '3.2496'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B89 / R89C2: '12'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G89 / R89C7: '4.432'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J89 / R89C10: '1.6657'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B90 / R90C2: '13'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B91 / R91C2: '14'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B92 / R92C2: '15'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B93 / R93C2: '16'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B94 / R94C2: '17'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G94 / R94C7: '4.408'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J94 / R94C10: '335.2297'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B95 / R95C2: '18'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G95 / R95C7: '4.419'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J95 / R95C10: '169.6308'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B96 / R96C2: '19'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G96 / R96C7: '4.427'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J96 / R96C10: '86.9693'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B97 / R97C2: '20'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G97 / R97C7: '4.430'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J97 / R97C10: '45.1144'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B98 / R98C2: '21'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G98 / R98C7: '4.430'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J98 / R98C10: '22.1038'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B99 / R99C2: '22'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G99 / R99C7: '4.432'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J99 / R99C10: '10.9339'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B100 / R100C2: '23'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G100 / R100C7: '4.433'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J100 / R100C10: '5.4531'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B101 / R101C2: '24'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G101 / R101C7: '4.434'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J101 / R101C10: '2.8113'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B102 / R102C2: '25'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G102 / R102C7: '4.435'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J102 / R102C10: '1.3821'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B103 / R103C2: '26'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B104 / R104C2: '27'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B105 / R105C2: '28'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B106 / R106C2: '29'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B107 / R107C2: '30'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G107 / R107C7: '4.422'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J107 / R107C10: '123.0908'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B108 / R108C2: '31'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G108 / R108C7: '4.422'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J108 / R108C10: '129.7855'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B109 / R109C2: '32'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G109 / R109C7: '4.434'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J109 / R109C10: '7.5666'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B110 / R110C2: '33'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G110 / R110C7: '4.433'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J110 / R110C10: '7.1015'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B111 / R111C2: '34'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G111 / R111C7: '4.434'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J111 / R111C10: '2.1369'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in B112 / R112C2: '35'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in G112 / R112C7: '4.434'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Coercing text to numeric in J112 / R112C10: '2.2197'

setClass('sample.prep',
         slots = list(compound='character', n.cal='numeric', reps='numeric'))
tanofivir.prep = new('sample.prep', compound='tanofivir', n.cal=12, reps=2)
rilpivirine.prep = tanofivir.prep
rilpivirine.prep@compound = 'rilpivirine'

n = rilpivirine.prep@n.cal
data.rilpivirine.1 = data.rilpivirine %>%
    cbind('stock' = c(rep(1, n), NA, rep(2, n), NA, rep(seq(3, 4), 3))) %>%
    cbind('type' = 
          c(rep(
              c(rep('Cal', n), 'blank'), 2),
            rep('QC', 6))
    ) %>%
    cbind('concentration' = c(
        rep(c(200/2^(seq_len(12)-1), 0), 2),
        rep(c(75, 3, 1), each = 2)
    ))

data.tanofivir.1 = data.tanofivir %>%
    cbind('stock' = c(rep(1, n), NA, rep(2, n), NA, rep(seq(3, 4), 3))) %>%
    cbind('type' =
              c(rep(
                  c(rep('Cal', n), 'blank'), 2),
                rep('QC', 6))
    ) %>%
    cbind('concentration' = c(
        rep(c(200/2^(seq_len(12)-1), 0), 2),
        rep(c(75, 3, 1), each = 2)
    ))

rilpivirine.group = data.rilpivirine.1 %>% group_by(stock)
tanofivir.group = data.tanofivir.1 %>% group_by(stock)

rilpivirine.group.cal = rilpivirine.group %>%
    filter(type == 'Cal')
cal.curve.rilpivirine = lm(Area ~ concentration, data = rilpivirine.group.cal, weights = 1/concentration)
summary(cal.curve.rilpivirine)

## 
## Call:
## lm(formula = Area ~ concentration, data = rilpivirine.group.cal, 
##     weights = 1/concentration)
## 
## Weighted Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.6158 -1.5489 -0.4529  0.9609  3.9240 
## 
## Coefficients:
##               Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   -0.87302    1.11199  -0.785    0.444    
## concentration  4.33438    0.08896  48.723   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.412 on 16 degrees of freedom
##   (6 observations deleted due to missingness)
## Multiple R-squared:  0.9933, Adjusted R-squared:  0.9929 
## F-statistic:  2374 on 1 and 16 DF,  p-value: < 2.2e-16

tanofivir.group.cal = tanofivir.group %>%
    filter(type == 'Cal')
cal.curve.tanofivir = lm(Area ~ concentration, data = tanofivir.group.cal, weights = 1/concentration)
summary(cal.curve.tanofivir)

## 
## Call:
## lm(formula = Area ~ concentration, data = tanofivir.group.cal, 
##     weights = 1/concentration)
## 
## Weighted Residuals:
##     Min      1Q  Median      3Q     Max 
## -7.9703 -1.1553  0.2077  1.6548  6.1099 
## 
## Coefficients:
##               Estimate Std. Error t value Pr(>|t|)    
## (Intercept)    -4.8082     0.9344  -5.146 6.78e-05 ***
## concentration  23.1212     0.1057 218.719  < 2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.915 on 18 degrees of freedom
##   (4 observations deleted due to missingness)
## Multiple R-squared:  0.9996, Adjusted R-squared:  0.9996 
## F-statistic: 4.784e+04 on 1 and 18 DF,  p-value: < 2.2e-16

cal.plot.rilpivirine = ggplot(rilpivirine.group, mapping = aes(concentration, Area)) +
    geom_point(aes(colour = stock, shape = type)) +
#    stat
    geom_smooth(data = rilpivirine.group.cal, 
        method = 'lm', mapping = aes(weight = 1/concentration), 
        formula = y ~ x, ) +
    labs(title='rilpivirine calibration', x='concentration, ug/mL',
         y='area, mAU*s') +
    theme_classic()
#cal.plot
#
#cal.plotly = plot_ly(data = data.group, x = ~concentration, y = ~Area,
#                     color = ~stock, colors = "Reds", symbol = ~type)
#cal.plotly
cal.plot.rilpivirine

## Warning: Removed 6 rows containing non-finite values (stat_smooth).

## Warning: Removed 8 rows containing missing values (geom_point).

ggplotly(cal.plot.rilpivirine)

## Warning: Removed 6 rows containing non-finite values (stat_smooth).

cal.plot.tanofivir = ggplot(tanofivir.group, mapping = aes(concentration, Area)) +
    geom_point(aes(colour = stock, shape = type)) +
#    stat
    geom_smooth(data = tanofivir.group.cal, 
        method = 'lm', mapping = aes(weight = 1/concentration), 
        formula = y ~ x, ) +
    labs(title='tanofivir calibration', x='concentration, ug/mL',
         y='area, mAU*s') +
    theme_classic()
cal.plot.tanofivir

## Warning: Removed 4 rows containing non-finite values (stat_smooth).

## Warning: Removed 6 rows containing missing values (geom_point).

ggplotly(cal.plot.tanofivir)

## Warning: Removed 4 rows containing non-finite values (stat_smooth).

data.post.rilpivirine = rilpivirine.group %>%
    mutate(calc.conc = (Area - cal.curve.rilpivirine$coefficients[1])/
               cal.curve.rilpivirine$coefficients[2],
           accuracy = calc.conc/concentration)
data.post.rilpivirine

data.post.rilpivirine.stock = data.post.rilpivirine %>% group_by(stock) %>%
    summarise(avg.acc = mean(accuracy))
data.post.rilpivirine.stock

data.post.tanofivir = tanofivir.group %>%
    mutate(calc.conc = (Area - cal.curve.tanofivir$coefficients[1])/
               cal.curve.tanofivir$coefficients[2],
           accuracy = calc.conc/concentration)
data.post.tanofivir

data.post.tanofivir.stock = data.post.tanofivir %>% group_by(stock) %>%
    summarise(avg.acc = mean(accuracy))
data.post.tanofivir.stock